9IBY | pdb_00009iby

Crystal structure of Zika Virus NS2B-NS3 protease in complex with compound 2

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5LC0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.75	293.15	12.00 %w/v PEG 8K 20.00 %v/v Glycerol 0.16 M Mg Acet 0.08 M Na Cacod

Crystal Properties
Matthews coefficient	Solvent content
2.62	53.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.793	α = 90
b = 57.472	β = 96.406
c = 72.447	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293.15	PIXEL	DECTRIS EIGER2 X 9M		2025-01-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.88560	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.291	44.961	89.6	0.141	0.995	6.8	6.6		14363

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.291	2.581			1.53	0.508

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.291	44.956	14363	733	62.617	0.191	0.189	0.1948	0.2357	0.2382	48.785

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
0.091		-0.593	0.386		-0.335

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_other_6_deg	18.356
r_dihedral_angle_2_deg	14.173
r_dihedral_angle_3_deg	12.328
r_dihedral_angle_6_deg	12.19
r_lrange_it	7.452
r_lrange_other	7.445
r_dihedral_angle_1_deg	7.022
r_mcangle_it	5.041
r_mcangle_other	5.04
r_scangle_it	4.806
r_scangle_other	4.804
r_mcbond_other	2.953
r_mcbond_it	2.952
r_scbond_it	2.891
r_scbond_other	2.89
r_angle_refined_deg	1.282
r_angle_other_deg	0.513
r_symmetry_nbd_other	0.174
r_nbd_refined	0.171
r_nbtor_refined	0.168
r_nbd_other	0.153
r_xyhbond_nbd_refined	0.148
r_symmetry_nbd_refined	0.102
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.066
r_ncsr_local_group_1	0.034
r_ext_dist_refined_b	0.015
r_symmetry_xyhbond_nbd_other	0.007
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2462
Nucleic Acid Atoms
Solvent Atoms	54
Heterogen Atoms	80

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
XSCALE	data scaling
PHENIX	phasing